Chemical amplification based on fluid partitioning

Abstract

A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

The invention claimed is: 
     
       1. An apparatus for nucleic acid amplification of a sample, comprising:
 means for partitioning said sample into partitioned sections, wherein said means for partitioning said sample into partitioned sections comprises an injection orifice, and   means for performing PCR on said partitioned sections of said sample.   
     
     
       2. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said injection orifice is an injection orifice that produces microdroplets. 
     
     
       3. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said injection orifice is an injection orifice that injects said sample and a PCR reagent. 
     
     
       4. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said means for performing PCR on said partitioned sections of said sample comprises a continuous tube for circulating said partitioned sections of said sample through a heater to perform PCR. 
     
     
       5. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said means for performing PCR on said partitioned sections of said sample comprises a continuous tube for circulating said partitioned sections of said sample through a heater and cooler to perform PCR. 
     
     
       6. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said means for performing PCR on said partitioned sections of said sample comprises a pump, a continuous tube, and a heater. 
     
     
       7. The apparatus for nucleic acid amplification of a sample of  claim 1  including means for detection and analysis of said partitioned sections of said sample comprising a laser and a detector. 
     
     
       8. The apparatus for nucleic acid amplification of a sample of  claim 1  including means for detection and analysis of said partitioned sections of said sample comprising a blue laser and a detector. 
     
     
       9. The apparatus for nucleic acid amplification of a sample of  claim 1  wherein said means for partitioning said sample into partitioned sections comprises means for separating said sample into immiscible slugs. 
     
     
       10. A method of nucleic acid amplification of a sample, comprising the steps of:
 partitioning said sample into partitioned sections, wherein said step of partitioning said sample into partitioned sections comprises flowing said sample through an injection orifice, and   subjecting said partitioned sections of said sample to PCR.   
     
     
       11. A method of nucleic acid amplification of a sample, comprising the steps of:
 a. partitioning the sample into partitioned sections, wherein partitioning comprises flowing the sample through an injection orifice into an immiscible carrier fluid, wherein the sample comprises a nucleic acid and components for performing nucleic acid amplification, wherein the partitioned sections comprise a gelling agent or a gel; and   b. moving the partitioned sections between a first substrate and a second substrate; and   c. performing nucleic acid amplification of the partitioned sections between the first substrate and the second substrate.   
     
     
       12. The method of claim 11, wherein the injection orifice is a microdroplet generator orifice connecting a sample flow pathway to a channel or tube comprising the immiscible carrier fluid and said flowing generates the partitioned sections, wherein the partitioned sections comprise microdroplets. 
     
     
       13. The method of claim 11, wherein said moving comprises gelling the partitioned sections in a thin layer between the first substrate and the second substrate. 
     
     
       14. The method of claim 11, wherein the first substrate and the second substrate comprise flat plates. 
     
     
       15. The method of claim 14, wherein the flat plates are conducive to optically probing the thin layer spatially in directions parallel to the thin layer's surface. 
     
     
       16. The method of claim 11, wherein either the first substrate or the second substrate comprise a solid support comprising small indentations arranged in a two-dimensional array. 
     
     
       17. The method of claim 16, wherein the solid support is hydrophobic. 
     
     
       18. The method of claim 16, wherein said moving comprises arranging the partitioned sections in said small indentations arranged in the two-dimensional array. 
     
     
       19. The method of claim 11, wherein said moving comprises using a pump. 
     
     
       20. The method of claim 11, wherein the first substrate and the second substrate are arranged to form microchannels. 
     
     
       21. The method of claim 11, wherein the nucleic acid amplification comprises amplification of a DNA target. 
     
     
       22. The method of claim 21, wherein the partitioned sections contain, on average, a single template of a DNA target, and wherein the single template is amplified within the partitioned sections. 
     
     
       23. The method of claim 11, further comprising detecting products of the nucleic acid amplification. 
     
     
       24. The method of claim 23, wherein the detecting comprises optically detecting. 
     
     
       25. The method of claim 24, wherein the optically detecting comprises confocal imaging. 
     
     
       26. The method of claim 24, wherein the optically detecting comprises laser excitation. 
     
     
       27. The method of claim 24, wherein the partitioned sections are probed for fluorescent signal. 
     
     
       28. The method of claim 11, wherein the nucleic acid amplification comprises multiple heating and cooling cycles. 
     
     
       29. The method of claim 28, wherein the number of cycles is sufficient to detect products of the nucleic acid amplification. 
     
     
       30. The method of claim 11, wherein the partitioned sections have a volume of about 5×10 −9  to 10 −12  liters.